Starting phenix.real_space_refine on Fri Sep 11 16:47:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6rag_4774/09_2026/6rag_4774.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rag_4774/09_2026/6rag_4774.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6rag_4774/09_2026/6rag_4774.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rag_4774/09_2026/6rag_4774.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6rag_4774/09_2026/6rag_4774.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rag_4774/09_2026/6rag_4774.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6rag_4774/09_2026/6rag_4774.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6rag_4774/09_2026/6rag_4774.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 5 5.49 5 Mg 2 5.21 5 S 25 5.16 5 C 6568 2.51 5 N 1797 2.21 5 O 1791 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10188 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 4690 Classifications: {'peptide': 586} Link IDs: {'PTRANS': 24, 'TRANS': 561} Chain: "B" Number of atoms: 4541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4541 Classifications: {'peptide': 575} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 556} Chain: "C" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 897 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.14, per 1000 atoms: 0.21 Number of scatterers: 10188 At special positions: 0 Unit cell: (102.315, 92.622, 155.088, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 25 16.00 P 5 15.00 Mg 2 11.99 O 1791 8.00 N 1797 7.00 C 6568 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 108 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 311.9 milliseconds 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2346 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 6 sheets defined 65.2% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 11 through 23 removed outlier: 4.261A pdb=" N ILE A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 45 Processing helix chain 'A' and resid 46 through 56 removed outlier: 4.178A pdb=" N PHE A 50 " --> pdb=" O THR A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 76 removed outlier: 5.012A pdb=" N LEU A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 74 " --> pdb=" O PHE A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 119 Processing helix chain 'A' and resid 123 through 128 removed outlier: 3.610A pdb=" N ARG A 127 " --> pdb=" O GLY A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 173 removed outlier: 4.341A pdb=" N LEU A 133 " --> pdb=" O PRO A 129 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR A 138 " --> pdb=" O MET A 134 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP A 140 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N VAL A 141 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP A 142 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU A 152 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER A 173 " --> pdb=" O MET A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 181 removed outlier: 4.461A pdb=" N VAL A 179 " --> pdb=" O LYS A 175 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 222 Processing helix chain 'A' and resid 222 through 229 Processing helix chain 'A' and resid 231 through 258 removed outlier: 3.742A pdb=" N LEU A 242 " --> pdb=" O LYS A 238 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP A 256 " --> pdb=" O GLU A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 286 Processing helix chain 'A' and resid 289 through 304 removed outlier: 3.657A pdb=" N VAL A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE A 304 " --> pdb=" O THR A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 307 No H-bonds generated for 'chain 'A' and resid 305 through 307' Processing helix chain 'A' and resid 308 through 313 removed outlier: 3.771A pdb=" N ASP A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 332 removed outlier: 3.645A pdb=" N GLY A 319 " --> pdb=" O ASN A 315 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG A 326 " --> pdb=" O ALA A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 374 Processing helix chain 'A' and resid 398 through 407 Processing helix chain 'A' and resid 425 through 427 No H-bonds generated for 'chain 'A' and resid 425 through 427' Processing helix chain 'A' and resid 428 through 435 removed outlier: 3.771A pdb=" N HIS A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 455 Processing helix chain 'A' and resid 462 through 473 removed outlier: 3.861A pdb=" N VAL A 466 " --> pdb=" O PRO A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 480 Processing helix chain 'A' and resid 498 through 514 removed outlier: 3.774A pdb=" N VAL A 508 " --> pdb=" O LEU A 504 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N SER A 514 " --> pdb=" O ALA A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 544 Processing helix chain 'A' and resid 555 through 562 Processing helix chain 'A' and resid 579 through 586 Processing helix chain 'A' and resid 587 through 594 Processing helix chain 'B' and resid 5 through 18 removed outlier: 4.006A pdb=" N LEU B 9 " --> pdb=" O SER B 5 " (cutoff:3.500A) Proline residue: B 15 - end of helix Processing helix chain 'B' and resid 20 through 54 Proline residue: B 42 - end of helix removed outlier: 4.006A pdb=" N ALA B 54 " --> pdb=" O ASP B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 105 removed outlier: 4.111A pdb=" N TYR B 61 " --> pdb=" O GLY B 57 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER B 72 " --> pdb=" O SER B 68 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VAL B 85 " --> pdb=" O ARG B 81 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N THR B 104 " --> pdb=" O HIS B 100 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU B 105 " --> pdb=" O HIS B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 113 removed outlier: 3.774A pdb=" N TYR B 110 " --> pdb=" O ASP B 106 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LYS B 112 " --> pdb=" O ASP B 108 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N HIS B 113 " --> pdb=" O PHE B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 133 Processing helix chain 'B' and resid 134 through 158 removed outlier: 3.534A pdb=" N PHE B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU B 148 " --> pdb=" O SER B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 207 removed outlier: 3.658A pdb=" N TYR B 164 " --> pdb=" O ARG B 160 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE B 168 " --> pdb=" O TYR B 164 " (cutoff:3.500A) Proline residue: B 170 - end of helix removed outlier: 3.563A pdb=" N PHE B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG B 185 " --> pdb=" O ARG B 181 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY B 207 " --> pdb=" O GLU B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 214 Processing helix chain 'B' and resid 216 through 243 removed outlier: 3.763A pdb=" N ALA B 222 " --> pdb=" O ARG B 218 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 271 removed outlier: 4.564A pdb=" N ALA B 247 " --> pdb=" O GLY B 243 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA B 256 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 288 removed outlier: 3.631A pdb=" N LEU B 278 " --> pdb=" O SER B 274 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 285 " --> pdb=" O PHE B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 316 Processing helix chain 'B' and resid 376 through 384 removed outlier: 4.146A pdb=" N VAL B 384 " --> pdb=" O LEU B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 412 Processing helix chain 'B' and resid 427 through 433 removed outlier: 3.804A pdb=" N ALA B 433 " --> pdb=" O LEU B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 436 No H-bonds generated for 'chain 'B' and resid 434 through 436' Processing helix chain 'B' and resid 440 through 451 removed outlier: 3.659A pdb=" N VAL B 444 " --> pdb=" O ASP B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 458 Processing helix chain 'B' and resid 462 through 466 removed outlier: 4.270A pdb=" N GLU B 465 " --> pdb=" O LYS B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 491 removed outlier: 3.615A pdb=" N LYS B 491 " --> pdb=" O ARG B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 519 Processing helix chain 'B' and resid 532 through 539 removed outlier: 3.568A pdb=" N ALA B 535 " --> pdb=" O ARG B 532 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N HIS B 538 " --> pdb=" O ALA B 535 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA B 539 " --> pdb=" O LEU B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 560 Processing helix chain 'B' and resid 564 through 578 removed outlier: 3.681A pdb=" N GLU B 568 " --> pdb=" O GLY B 564 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.924A pdb=" N THR C 91 " --> pdb=" O PRO C 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 379 through 383 removed outlier: 4.979A pdb=" N VAL A 379 " --> pdb=" O ASP A 357 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 353 " --> pdb=" O VAL A 383 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL A 358 " --> pdb=" O ARG A 414 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ARG A 414 " --> pdb=" O VAL A 358 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 436 through 439 removed outlier: 5.774A pdb=" N LEU A 519 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ILE A 552 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LEU A 521 " --> pdb=" O ILE A 552 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL A 389 " --> pdb=" O ILE A 551 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ARG A 569 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LEU A 573 " --> pdb=" O ARG A 569 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 354 through 361 removed outlier: 4.474A pdb=" N LEU B 354 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N VAL B 344 " --> pdb=" O GLY B 356 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N THR B 358 " --> pdb=" O GLU B 342 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLU B 342 " --> pdb=" O THR B 358 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N THR B 360 " --> pdb=" O ARG B 340 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ARG B 340 " --> pdb=" O THR B 360 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N PHE B 341 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N TYR B 396 " --> pdb=" O PHE B 341 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N GLY B 343 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ARG B 394 " --> pdb=" O GLY B 343 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 414 through 417 removed outlier: 6.091A pdb=" N GLY B 415 " --> pdb=" O ILE B 497 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ASP B 499 " --> pdb=" O GLY B 415 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ALA B 417 " --> pdb=" O ASP B 499 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU B 496 " --> pdb=" O LEU B 527 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ILE B 529 " --> pdb=" O LEU B 496 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU B 498 " --> pdb=" O ILE B 529 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LEU B 367 " --> pdb=" O LEU B 528 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TRP B 541 " --> pdb=" O THR B 366 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU B 545 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA C 101 " --> pdb=" O VAL C 109 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.660A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.529A pdb=" N ALA C 92 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ARG C 38 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N GLY C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) 634 hydrogen bonds defined for protein. 1863 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.48 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1615 1.31 - 1.44: 2800 1.44 - 1.56: 5924 1.56 - 1.69: 16 1.69 - 1.81: 45 Bond restraints: 10400 Sorted by residual: bond pdb=" C4 ATP B 602 " pdb=" C5 ATP B 602 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.79e+01 bond pdb=" C5 ATP B 602 " pdb=" C6 ATP B 602 " ideal model delta sigma weight residual 1.409 1.474 -0.065 1.00e-02 1.00e+04 4.21e+01 bond pdb=" N PRO A 515 " pdb=" CD PRO A 515 " ideal model delta sigma weight residual 1.473 1.556 -0.083 1.40e-02 5.10e+03 3.55e+01 bond pdb=" CA PHE A 296 " pdb=" C PHE A 296 " ideal model delta sigma weight residual 1.522 1.593 -0.071 1.39e-02 5.18e+03 2.57e+01 bond pdb=" C4 ATP B 602 " pdb=" N9 ATP B 602 " ideal model delta sigma weight residual 1.374 1.326 0.048 1.00e-02 1.00e+04 2.30e+01 ... (remaining 10395 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.99: 13772 3.99 - 7.98: 292 7.98 - 11.96: 44 11.96 - 15.95: 1 15.95 - 19.94: 2 Bond angle restraints: 14111 Sorted by residual: angle pdb=" PB ATP B 602 " pdb=" O3B ATP B 602 " pdb=" PG ATP B 602 " ideal model delta sigma weight residual 139.87 119.93 19.94 1.00e+00 1.00e+00 3.98e+02 angle pdb=" PA ATP B 602 " pdb=" O3A ATP B 602 " pdb=" PB ATP B 602 " ideal model delta sigma weight residual 136.83 118.46 18.37 1.00e+00 1.00e+00 3.37e+02 angle pdb=" N VAL B 298 " pdb=" CA VAL B 298 " pdb=" C VAL B 298 " ideal model delta sigma weight residual 110.53 98.04 12.49 9.40e-01 1.13e+00 1.77e+02 angle pdb=" N GLY B 296 " pdb=" CA GLY B 296 " pdb=" C GLY B 296 " ideal model delta sigma weight residual 112.64 123.80 -11.16 1.21e+00 6.83e-01 8.51e+01 angle pdb=" N LEU B 536 " pdb=" CA LEU B 536 " pdb=" C LEU B 536 " ideal model delta sigma weight residual 112.97 103.27 9.70 1.06e+00 8.90e-01 8.37e+01 ... (remaining 14106 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.84: 5924 29.84 - 59.67: 212 59.67 - 89.51: 22 89.51 - 119.34: 1 119.34 - 149.17: 2 Dihedral angle restraints: 6161 sinusoidal: 2496 harmonic: 3665 Sorted by residual: dihedral pdb=" O1B ADP A 702 " pdb=" O3A ADP A 702 " pdb=" PB ADP A 702 " pdb=" PA ADP A 702 " ideal model delta sinusoidal sigma weight residual 300.00 150.82 149.17 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" O2A ADP A 702 " pdb=" O3A ADP A 702 " pdb=" PA ADP A 702 " pdb=" PB ADP A 702 " ideal model delta sinusoidal sigma weight residual -60.00 62.82 -122.82 1 2.00e+01 2.50e-03 3.70e+01 dihedral pdb=" CA TRP B 290 " pdb=" C TRP B 290 " pdb=" N PRO B 291 " pdb=" CA PRO B 291 " ideal model delta harmonic sigma weight residual -180.00 -150.78 -29.22 0 5.00e+00 4.00e-02 3.42e+01 ... (remaining 6158 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1335 0.096 - 0.191: 229 0.191 - 0.287: 29 0.287 - 0.383: 9 0.383 - 0.478: 7 Chirality restraints: 1609 Sorted by residual: chirality pdb=" CA ASP B 500 " pdb=" N ASP B 500 " pdb=" C ASP B 500 " pdb=" CB ASP B 500 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.72e+00 chirality pdb=" CA VAL C 102 " pdb=" N VAL C 102 " pdb=" C VAL C 102 " pdb=" CB VAL C 102 " both_signs ideal model delta sigma weight residual False 2.44 2.90 -0.46 2.00e-01 2.50e+01 5.37e+00 chirality pdb=" CA LEU C 104 " pdb=" N LEU C 104 " pdb=" C LEU C 104 " pdb=" CB LEU C 104 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.36e+00 ... (remaining 1606 not shown) Planarity restraints: 1785 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 138 " 0.023 2.00e-02 2.50e+03 4.74e-02 2.25e+01 pdb=" C THR A 138 " -0.082 2.00e-02 2.50e+03 pdb=" O THR A 138 " 0.031 2.00e-02 2.50e+03 pdb=" N SER A 139 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP A 23 " -0.052 5.00e-02 4.00e+02 7.84e-02 9.84e+00 pdb=" N PRO A 24 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 24 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 24 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 243 " -0.048 5.00e-02 4.00e+02 7.16e-02 8.19e+00 pdb=" N PRO B 244 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO B 244 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 244 " -0.040 5.00e-02 4.00e+02 ... (remaining 1782 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 32 2.51 - 3.11: 7067 3.11 - 3.70: 15963 3.70 - 4.30: 21137 4.30 - 4.90: 34422 Nonbonded interactions: 78621 Sorted by model distance: nonbonded pdb="MG MG B 601 " pdb=" O1B ATP B 602 " model vdw 1.911 2.170 nonbonded pdb="MG MG B 601 " pdb=" O1G ATP B 602 " model vdw 1.923 2.170 nonbonded pdb=" OE1 GLN B 419 " pdb="MG MG B 601 " model vdw 2.024 2.170 nonbonded pdb=" OG SER B 378 " pdb="MG MG B 601 " model vdw 2.050 2.170 nonbonded pdb=" O THR A 400 " pdb=" OG SER A 404 " model vdw 2.252 3.040 ... (remaining 78616 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.060 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.103 10402 Z= 0.510 Angle : 1.420 19.938 14115 Z= 0.926 Chirality : 0.079 0.478 1609 Planarity : 0.008 0.078 1785 Dihedral : 15.365 149.175 3809 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.67 % Allowed : 12.20 % Favored : 87.13 % Cbeta Deviations : 0.43 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.67 (0.18), residues: 1276 helix: -2.48 (0.14), residues: 768 sheet: -0.57 (0.43), residues: 124 loop : -2.52 (0.27), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 235 TYR 0.029 0.003 TYR A 588 PHE 0.025 0.003 PHE A 147 TRP 0.038 0.003 TRP A 193 HIS 0.012 0.002 HIS B 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00968 / 0.51 (10400) covalent geometry : angle 1.41955 / 0.93 (14111) SS BOND : bond 0.02172 / 1.03 ( 2) SS BOND : angle 2.02293 / 1.12 ( 4) hydrogen bonds : bond 0.17221 / 11.30 ( 634) hydrogen bonds : angle 6.95447 / 5.16 ( 1863) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 273 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 PHE cc_start: 0.7288 (m-10) cc_final: 0.7011 (m-80) REVERT: A 118 MET cc_start: 0.9224 (mmt) cc_final: 0.9007 (tpp) REVERT: A 166 LEU cc_start: 0.8440 (tp) cc_final: 0.7963 (tt) REVERT: A 205 MET cc_start: 0.8817 (tmm) cc_final: 0.8548 (tmm) REVERT: A 218 GLU cc_start: 0.8421 (tt0) cc_final: 0.8138 (tm-30) REVERT: A 375 VAL cc_start: 0.0141 (OUTLIER) cc_final: -0.0356 (t) REVERT: A 430 GLU cc_start: 0.8154 (pt0) cc_final: 0.7393 (mt-10) REVERT: A 508 VAL cc_start: 0.8884 (p) cc_final: 0.8680 (m) REVERT: A 560 ARG cc_start: 0.8851 (mmm-85) cc_final: 0.8473 (tpp80) REVERT: B 25 LEU cc_start: 0.8800 (tp) cc_final: 0.8360 (tt) REVERT: B 32 LEU cc_start: 0.8446 (mt) cc_final: 0.8211 (mp) REVERT: B 154 MET cc_start: 0.8952 (ttt) cc_final: 0.8295 (ttt) REVERT: B 191 GLN cc_start: 0.8146 (pp30) cc_final: 0.7894 (tm-30) REVERT: B 228 ASN cc_start: 0.9239 (t0) cc_final: 0.8896 (t0) REVERT: B 347 LYS cc_start: 0.7606 (tptt) cc_final: 0.7004 (tppt) REVERT: B 412 LYS cc_start: 0.9029 (ttmt) cc_final: 0.8478 (mtmm) REVERT: B 436 LEU cc_start: 0.9108 (tp) cc_final: 0.8888 (tp) REVERT: B 521 LEU cc_start: 0.8826 (tp) cc_final: 0.8470 (mp) REVERT: B 558 SER cc_start: 0.9096 (m) cc_final: 0.8819 (t) REVERT: B 559 LEU cc_start: 0.9062 (mt) cc_final: 0.8796 (mt) REVERT: B 569 MET cc_start: 0.6915 (ttm) cc_final: 0.6458 (ttm) REVERT: C 37 PHE cc_start: 0.8313 (m-80) cc_final: 0.8091 (m-80) REVERT: C 53 LYS cc_start: 0.8974 (ttpp) cc_final: 0.8765 (ttmt) REVERT: C 93 VAL cc_start: 0.8760 (m) cc_final: 0.8357 (p) REVERT: C 98 THR cc_start: 0.8955 (m) cc_final: 0.8628 (t) REVERT: C 109 VAL cc_start: 0.8536 (t) cc_final: 0.8227 (t) outliers start: 7 outliers final: 4 residues processed: 279 average time/residue: 0.1202 time to fit residues: 45.1702 Evaluate side-chains 186 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 181 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 123 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 GLN A 453 ASN ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 HIS ** B 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 ASN B 479 GLN B 531 HIS B 556 HIS C 3 GLN C 39 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.116567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.088839 restraints weight = 26034.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.091181 restraints weight = 16812.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.092741 restraints weight = 12463.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.093845 restraints weight = 10204.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.094512 restraints weight = 8900.321| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10402 Z= 0.145 Angle : 0.678 6.727 14115 Z= 0.347 Chirality : 0.043 0.171 1609 Planarity : 0.006 0.064 1785 Dihedral : 6.891 114.537 1452 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.29 % Allowed : 5.82 % Favored : 93.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.22), residues: 1276 helix: -0.37 (0.17), residues: 778 sheet: -0.73 (0.40), residues: 138 loop : -1.85 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 428 TYR 0.023 0.001 TYR A 588 PHE 0.021 0.001 PHE A 160 TRP 0.026 0.002 TRP A 193 HIS 0.011 0.001 HIS B 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 (10400) covalent geometry : angle 0.67804 / 0.35 (14111) SS BOND : bond 0.00296 / 0.15 ( 2) SS BOND : angle 0.51403 / 0.23 ( 4) hydrogen bonds : bond 0.05122 / 3.39 ( 634) hydrogen bonds : angle 4.82867 / 3.55 ( 1863) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 251 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 LEU cc_start: 0.6132 (mt) cc_final: 0.5882 (mt) REVERT: A 445 LEU cc_start: 0.8084 (mm) cc_final: 0.7856 (tp) REVERT: B 25 LEU cc_start: 0.8644 (tp) cc_final: 0.8380 (tt) REVERT: B 32 LEU cc_start: 0.8287 (mt) cc_final: 0.7646 (mt) REVERT: B 108 ASP cc_start: 0.7556 (t70) cc_final: 0.6853 (t0) REVERT: B 154 MET cc_start: 0.8741 (ttt) cc_final: 0.8032 (ttt) REVERT: B 252 LEU cc_start: 0.9234 (mm) cc_final: 0.8970 (mm) REVERT: B 347 LYS cc_start: 0.7245 (tptt) cc_final: 0.6580 (tppt) REVERT: B 365 MET cc_start: 0.8070 (tmm) cc_final: 0.7752 (tmm) REVERT: B 380 LEU cc_start: 0.8739 (tp) cc_final: 0.8510 (tp) REVERT: B 423 LEU cc_start: 0.8893 (mt) cc_final: 0.8579 (pp) REVERT: B 431 ASN cc_start: 0.7748 (OUTLIER) cc_final: 0.7346 (t0) REVERT: B 521 LEU cc_start: 0.8671 (tp) cc_final: 0.8206 (mp) REVERT: B 559 LEU cc_start: 0.9291 (mt) cc_final: 0.9082 (mt) REVERT: B 569 MET cc_start: 0.6888 (ttm) cc_final: 0.6316 (ttm) REVERT: C 3 GLN cc_start: 0.5483 (pt0) cc_final: 0.3919 (pt0) REVERT: C 57 ASN cc_start: 0.7315 (m-40) cc_final: 0.6839 (t0) REVERT: C 65 LYS cc_start: 0.8786 (ptmt) cc_final: 0.8373 (mttt) REVERT: C 93 VAL cc_start: 0.8544 (m) cc_final: 0.8159 (p) outliers start: 3 outliers final: 0 residues processed: 253 average time/residue: 0.1059 time to fit residues: 37.3664 Evaluate side-chains 174 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 173 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 99 optimal weight: 0.0000 chunk 43 optimal weight: 0.0370 chunk 64 optimal weight: 0.7980 chunk 29 optimal weight: 0.1980 chunk 71 optimal weight: 0.0870 chunk 95 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 96 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 overall best weight: 0.2040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 596 GLN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 ASN B 531 HIS B 538 HIS C 80 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.119256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.090809 restraints weight = 26420.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.093468 restraints weight = 16238.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.095276 restraints weight = 11605.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.096522 restraints weight = 9259.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.097113 restraints weight = 7922.940| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10402 Z= 0.123 Angle : 0.627 8.277 14115 Z= 0.314 Chirality : 0.041 0.164 1609 Planarity : 0.005 0.057 1785 Dihedral : 6.159 99.666 1452 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.23), residues: 1276 helix: 0.69 (0.18), residues: 769 sheet: -0.70 (0.39), residues: 135 loop : -1.40 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 532 TYR 0.016 0.001 TYR A 588 PHE 0.016 0.001 PHE B 281 TRP 0.020 0.002 TRP C 36 HIS 0.003 0.001 HIS B 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (10400) covalent geometry : angle 0.62715 / 0.31 (14111) SS BOND : bond 0.01371 / 0.66 ( 2) SS BOND : angle 1.21996 / 0.64 ( 4) hydrogen bonds : bond 0.04428 / 2.95 ( 634) hydrogen bonds : angle 4.30449 / 3.16 ( 1863) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 MET cc_start: 0.8784 (tmm) cc_final: 0.8560 (tmm) REVERT: A 376 LEU cc_start: 0.5908 (mt) cc_final: 0.5651 (mt) REVERT: A 417 VAL cc_start: 0.5437 (t) cc_final: 0.5137 (t) REVERT: A 444 PHE cc_start: 0.6864 (t80) cc_final: 0.6450 (t80) REVERT: B 25 LEU cc_start: 0.8619 (tp) cc_final: 0.8339 (tt) REVERT: B 32 LEU cc_start: 0.8068 (mt) cc_final: 0.7663 (mt) REVERT: B 125 ASP cc_start: 0.6654 (m-30) cc_final: 0.6454 (m-30) REVERT: B 154 MET cc_start: 0.8845 (ttt) cc_final: 0.7975 (ttt) REVERT: B 199 THR cc_start: 0.9004 (m) cc_final: 0.8640 (m) REVERT: B 228 ASN cc_start: 0.9114 (t0) cc_final: 0.8878 (t0) REVERT: B 347 LYS cc_start: 0.7359 (tptt) cc_final: 0.6700 (tppt) REVERT: B 365 MET cc_start: 0.8063 (tmm) cc_final: 0.7719 (tmm) REVERT: B 436 LEU cc_start: 0.8718 (tp) cc_final: 0.8510 (tp) REVERT: B 559 LEU cc_start: 0.9365 (mt) cc_final: 0.9146 (mt) REVERT: B 569 MET cc_start: 0.6795 (ttm) cc_final: 0.6185 (ttm) REVERT: C 3 GLN cc_start: 0.6249 (pt0) cc_final: 0.5944 (pt0) REVERT: C 65 LYS cc_start: 0.8977 (ptmt) cc_final: 0.8503 (mttt) REVERT: C 93 VAL cc_start: 0.8829 (m) cc_final: 0.8462 (p) REVERT: C 94 TYR cc_start: 0.5738 (m-10) cc_final: 0.5396 (m-80) outliers start: 0 outliers final: 0 residues processed: 247 average time/residue: 0.0903 time to fit residues: 32.3701 Evaluate side-chains 165 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 117 optimal weight: 8.9990 chunk 55 optimal weight: 7.9990 chunk 87 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 42 optimal weight: 6.9990 chunk 82 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 40 optimal weight: 0.0670 chunk 19 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 431 ASN B 538 HIS C 80 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.118283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.091505 restraints weight = 26282.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.093203 restraints weight = 17317.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.093687 restraints weight = 12019.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.094515 restraints weight = 12118.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.094675 restraints weight = 10408.157| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10402 Z= 0.127 Angle : 0.621 8.442 14115 Z= 0.310 Chirality : 0.042 0.313 1609 Planarity : 0.004 0.051 1785 Dihedral : 5.764 95.834 1452 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.23), residues: 1276 helix: 1.10 (0.18), residues: 778 sheet: -0.60 (0.38), residues: 143 loop : -1.28 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 127 TYR 0.039 0.001 TYR B 187 PHE 0.018 0.001 PHE A 160 TRP 0.024 0.001 TRP C 36 HIS 0.004 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (10400) covalent geometry : angle 0.62099 / 0.31 (14111) SS BOND : bond 0.00759 / 0.40 ( 2) SS BOND : angle 0.99504 / 0.51 ( 4) hydrogen bonds : bond 0.04229 / 2.83 ( 634) hydrogen bonds : angle 4.13456 / 3.03 ( 1863) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ASP cc_start: 0.8858 (t0) cc_final: 0.8304 (t70) REVERT: A 299 TYR cc_start: 0.8980 (m-80) cc_final: 0.8409 (m-80) REVERT: A 376 LEU cc_start: 0.6276 (mt) cc_final: 0.6016 (mt) REVERT: A 444 PHE cc_start: 0.6989 (t80) cc_final: 0.6653 (t80) REVERT: B 25 LEU cc_start: 0.8636 (tp) cc_final: 0.8418 (tt) REVERT: B 32 LEU cc_start: 0.8193 (mt) cc_final: 0.7653 (mt) REVERT: B 79 MET cc_start: 0.8882 (tmm) cc_final: 0.8642 (tmm) REVERT: B 154 MET cc_start: 0.8619 (ttt) cc_final: 0.7948 (ttt) REVERT: B 199 THR cc_start: 0.9001 (m) cc_final: 0.8596 (m) REVERT: B 347 LYS cc_start: 0.7392 (tptt) cc_final: 0.6783 (tppt) REVERT: B 365 MET cc_start: 0.8117 (tmm) cc_final: 0.7862 (tmm) REVERT: B 559 LEU cc_start: 0.9400 (mt) cc_final: 0.9170 (mt) REVERT: B 569 MET cc_start: 0.6954 (ttm) cc_final: 0.6234 (ttm) REVERT: C 3 GLN cc_start: 0.6315 (pt0) cc_final: 0.5970 (pt0) REVERT: C 65 LYS cc_start: 0.8957 (ptmt) cc_final: 0.8542 (mttt) REVERT: C 93 VAL cc_start: 0.8720 (m) cc_final: 0.8414 (t) REVERT: C 94 TYR cc_start: 0.5912 (m-10) cc_final: 0.5373 (m-80) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.0967 time to fit residues: 31.2125 Evaluate side-chains 159 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 10 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 120 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 GLN A 561 HIS B 53 GLN ** B 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 ASN C 80 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.112437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.085392 restraints weight = 26723.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.086724 restraints weight = 19271.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.087462 restraints weight = 14040.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.087588 restraints weight = 13160.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.087700 restraints weight = 12596.736| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 10402 Z= 0.200 Angle : 0.697 7.855 14115 Z= 0.347 Chirality : 0.044 0.189 1609 Planarity : 0.005 0.051 1785 Dihedral : 5.616 91.180 1452 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.23), residues: 1276 helix: 0.99 (0.18), residues: 777 sheet: -0.43 (0.41), residues: 122 loop : -1.21 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 244 TYR 0.027 0.002 TYR B 187 PHE 0.022 0.002 PHE A 478 TRP 0.029 0.002 TRP C 36 HIS 0.007 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.20 (10400) covalent geometry : angle 0.69717 / 0.35 (14111) SS BOND : bond 0.00881 / 0.46 ( 2) SS BOND : angle 1.36611 / 0.74 ( 4) hydrogen bonds : bond 0.04587 / 3.03 ( 634) hydrogen bonds : angle 4.44089 / 3.26 ( 1863) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 TYR cc_start: 0.9065 (m-80) cc_final: 0.8531 (m-80) REVERT: A 418 PHE cc_start: 0.7750 (m-80) cc_final: 0.7002 (m-10) REVERT: A 444 PHE cc_start: 0.7249 (t80) cc_final: 0.6883 (t80) REVERT: B 25 LEU cc_start: 0.8755 (tp) cc_final: 0.8482 (tt) REVERT: B 32 LEU cc_start: 0.8468 (mt) cc_final: 0.7694 (mt) REVERT: B 79 MET cc_start: 0.8958 (tmm) cc_final: 0.8700 (tmm) REVERT: B 154 MET cc_start: 0.8842 (ttt) cc_final: 0.8306 (ttt) REVERT: B 199 THR cc_start: 0.9026 (m) cc_final: 0.8624 (m) REVERT: B 365 MET cc_start: 0.8196 (tmm) cc_final: 0.7891 (tmm) REVERT: B 436 LEU cc_start: 0.8921 (tp) cc_final: 0.8715 (tp) REVERT: B 500 ASP cc_start: 0.7069 (m-30) cc_final: 0.6537 (m-30) REVERT: B 569 MET cc_start: 0.7159 (ttm) cc_final: 0.6439 (ttm) REVERT: C 65 LYS cc_start: 0.9017 (ptmt) cc_final: 0.8555 (mttt) REVERT: C 93 VAL cc_start: 0.8661 (m) cc_final: 0.8240 (p) REVERT: C 94 TYR cc_start: 0.6016 (m-10) cc_final: 0.5480 (m-80) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.1002 time to fit residues: 29.0604 Evaluate side-chains 149 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 78 optimal weight: 0.6980 chunk 99 optimal weight: 0.0070 chunk 34 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 82 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 431 ASN B 538 HIS C 80 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.116846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.089261 restraints weight = 26424.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.091686 restraints weight = 16318.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.093372 restraints weight = 11815.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.094513 restraints weight = 9491.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.095122 restraints weight = 8191.986| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10402 Z= 0.124 Angle : 0.631 7.642 14115 Z= 0.310 Chirality : 0.041 0.190 1609 Planarity : 0.004 0.050 1785 Dihedral : 5.101 73.859 1452 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.23), residues: 1276 helix: 1.42 (0.18), residues: 778 sheet: -0.56 (0.39), residues: 132 loop : -1.07 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 19 TYR 0.024 0.001 TYR B 187 PHE 0.021 0.001 PHE A 478 TRP 0.046 0.002 TRP C 36 HIS 0.003 0.001 HIS B 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (10400) covalent geometry : angle 0.63040 / 0.31 (14111) SS BOND : bond 0.00574 / 0.30 ( 2) SS BOND : angle 1.58409 / 0.83 ( 4) hydrogen bonds : bond 0.04224 / 2.83 ( 634) hydrogen bonds : angle 4.13040 / 3.03 ( 1863) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8949 (pp20) cc_final: 0.8641 (pp20) REVERT: A 299 TYR cc_start: 0.9007 (m-80) cc_final: 0.8474 (m-80) REVERT: A 405 LEU cc_start: 0.8216 (tp) cc_final: 0.7980 (tp) REVERT: A 444 PHE cc_start: 0.7251 (t80) cc_final: 0.6881 (t80) REVERT: A 455 ARG cc_start: 0.7677 (ptt-90) cc_final: 0.7472 (ptt-90) REVERT: B 25 LEU cc_start: 0.8650 (tp) cc_final: 0.8369 (tt) REVERT: B 32 LEU cc_start: 0.8242 (mt) cc_final: 0.7655 (mt) REVERT: B 79 MET cc_start: 0.8902 (tmm) cc_final: 0.8629 (tmm) REVERT: B 154 MET cc_start: 0.8667 (ttt) cc_final: 0.8032 (ttt) REVERT: B 199 THR cc_start: 0.8938 (m) cc_final: 0.8562 (m) REVERT: B 365 MET cc_start: 0.8155 (tmm) cc_final: 0.7808 (tmm) REVERT: B 499 ASP cc_start: 0.6263 (t70) cc_final: 0.5187 (t0) REVERT: B 528 LEU cc_start: 0.9226 (tp) cc_final: 0.9021 (tt) REVERT: B 559 LEU cc_start: 0.9401 (mt) cc_final: 0.9105 (mt) REVERT: B 569 MET cc_start: 0.6810 (ttm) cc_final: 0.6107 (ttm) REVERT: C 65 LYS cc_start: 0.8947 (ptmt) cc_final: 0.8499 (mttt) REVERT: C 93 VAL cc_start: 0.8546 (m) cc_final: 0.8057 (p) REVERT: C 94 TYR cc_start: 0.5840 (m-10) cc_final: 0.5375 (m-80) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.0965 time to fit residues: 29.1383 Evaluate side-chains 148 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 46 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 113 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 GLN B 431 ASN C 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.115080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.087265 restraints weight = 26251.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.089514 restraints weight = 17163.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.091042 restraints weight = 12804.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.092064 restraints weight = 10570.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.092654 restraints weight = 9315.884| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10402 Z= 0.142 Angle : 0.644 8.511 14115 Z= 0.316 Chirality : 0.042 0.186 1609 Planarity : 0.004 0.048 1785 Dihedral : 4.891 65.143 1452 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.10 % Allowed : 1.33 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.23), residues: 1276 helix: 1.45 (0.18), residues: 784 sheet: -0.42 (0.41), residues: 132 loop : -1.04 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 19 TYR 0.023 0.001 TYR B 187 PHE 0.022 0.001 PHE A 478 TRP 0.028 0.002 TRP C 36 HIS 0.004 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (10400) covalent geometry : angle 0.64415 / 0.32 (14111) SS BOND : bond 0.00487 / 0.26 ( 2) SS BOND : angle 1.27876 / 0.66 ( 4) hydrogen bonds : bond 0.04250 / 2.83 ( 634) hydrogen bonds : angle 4.20586 / 3.08 ( 1863) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 189 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.9005 (pp20) cc_final: 0.8708 (pp20) REVERT: A 112 ASP cc_start: 0.8878 (t0) cc_final: 0.8380 (t70) REVERT: A 205 MET cc_start: 0.8771 (tmm) cc_final: 0.8372 (tmm) REVERT: A 299 TYR cc_start: 0.8951 (m-80) cc_final: 0.8357 (m-80) REVERT: A 405 LEU cc_start: 0.8242 (tp) cc_final: 0.7989 (tp) REVERT: A 444 PHE cc_start: 0.7325 (t80) cc_final: 0.6878 (t80) REVERT: A 455 ARG cc_start: 0.7711 (ptt-90) cc_final: 0.7485 (ptt-90) REVERT: B 25 LEU cc_start: 0.8650 (tp) cc_final: 0.8381 (tt) REVERT: B 32 LEU cc_start: 0.8330 (mt) cc_final: 0.7647 (mt) REVERT: B 79 MET cc_start: 0.8831 (tmm) cc_final: 0.8554 (tmm) REVERT: B 154 MET cc_start: 0.8700 (ttt) cc_final: 0.8197 (ttt) REVERT: B 199 THR cc_start: 0.8998 (m) cc_final: 0.8632 (m) REVERT: B 365 MET cc_start: 0.8172 (tmm) cc_final: 0.7844 (tmm) REVERT: B 436 LEU cc_start: 0.8885 (tp) cc_final: 0.8658 (tp) REVERT: B 528 LEU cc_start: 0.9256 (tp) cc_final: 0.9011 (tt) REVERT: B 559 LEU cc_start: 0.9344 (mt) cc_final: 0.9063 (mt) REVERT: B 569 MET cc_start: 0.6875 (ttm) cc_final: 0.6182 (ttm) REVERT: C 65 LYS cc_start: 0.9047 (ptmt) cc_final: 0.8602 (mtpt) REVERT: C 72 ARG cc_start: 0.7672 (tmm160) cc_final: 0.7336 (tmm-80) REVERT: C 93 VAL cc_start: 0.8527 (m) cc_final: 0.8069 (p) REVERT: C 94 TYR cc_start: 0.5827 (m-10) cc_final: 0.5516 (m-80) outliers start: 1 outliers final: 0 residues processed: 189 average time/residue: 0.0947 time to fit residues: 25.7531 Evaluate side-chains 147 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 27 optimal weight: 0.0670 chunk 34 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 32 optimal weight: 8.9990 chunk 24 optimal weight: 0.3980 chunk 105 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 ASN B 431 ASN B 531 HIS C 3 GLN C 80 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.118988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.091626 restraints weight = 26433.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.094156 restraints weight = 16047.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.095758 restraints weight = 11477.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.097012 restraints weight = 9207.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.097787 restraints weight = 7882.498| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.4772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10402 Z= 0.119 Angle : 0.623 7.734 14115 Z= 0.305 Chirality : 0.041 0.188 1609 Planarity : 0.004 0.048 1785 Dihedral : 4.617 58.427 1452 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.10 % Allowed : 1.05 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.24), residues: 1276 helix: 1.62 (0.18), residues: 783 sheet: -0.42 (0.41), residues: 137 loop : -0.90 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 19 TYR 0.021 0.001 TYR B 187 PHE 0.020 0.001 PHE A 478 TRP 0.047 0.002 TRP C 36 HIS 0.003 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (10400) covalent geometry : angle 0.62274 / 0.30 (14111) SS BOND : bond 0.00577 / 0.30 ( 2) SS BOND : angle 1.20596 / 0.64 ( 4) hydrogen bonds : bond 0.04047 / 2.71 ( 634) hydrogen bonds : angle 4.05788 / 2.98 ( 1863) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 195 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ASP cc_start: 0.8880 (t0) cc_final: 0.8408 (t70) REVERT: A 205 MET cc_start: 0.8744 (tmm) cc_final: 0.8356 (tmm) REVERT: A 299 TYR cc_start: 0.8904 (m-80) cc_final: 0.8402 (m-80) REVERT: A 444 PHE cc_start: 0.7236 (t80) cc_final: 0.6820 (t80) REVERT: A 455 ARG cc_start: 0.7639 (ptt-90) cc_final: 0.7414 (ptt-90) REVERT: A 544 MET cc_start: 0.7703 (mmm) cc_final: 0.7217 (mmm) REVERT: B 25 LEU cc_start: 0.8675 (tp) cc_final: 0.8378 (tt) REVERT: B 32 LEU cc_start: 0.8239 (mt) cc_final: 0.7668 (mt) REVERT: B 79 MET cc_start: 0.8834 (tmm) cc_final: 0.8486 (tmm) REVERT: B 154 MET cc_start: 0.8727 (ttt) cc_final: 0.8194 (ttt) REVERT: B 199 THR cc_start: 0.8966 (m) cc_final: 0.8617 (m) REVERT: B 365 MET cc_start: 0.8226 (tmm) cc_final: 0.7901 (tmm) REVERT: B 436 LEU cc_start: 0.8926 (tp) cc_final: 0.8644 (tp) REVERT: B 559 LEU cc_start: 0.9329 (mt) cc_final: 0.9007 (mt) REVERT: B 569 MET cc_start: 0.6719 (ttm) cc_final: 0.6038 (ttm) REVERT: C 65 LYS cc_start: 0.8972 (ptmt) cc_final: 0.8450 (mttt) REVERT: C 93 VAL cc_start: 0.8593 (m) cc_final: 0.8145 (p) REVERT: C 94 TYR cc_start: 0.5801 (m-10) cc_final: 0.5534 (m-80) outliers start: 1 outliers final: 0 residues processed: 195 average time/residue: 0.0958 time to fit residues: 27.2080 Evaluate side-chains 144 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 88 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 109 optimal weight: 0.0970 chunk 53 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 116 optimal weight: 0.0670 chunk 69 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.5720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 ASN A 503 GLN B 431 ASN C 3 GLN C 80 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.118973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.091472 restraints weight = 26973.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.093975 restraints weight = 16617.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.095658 restraints weight = 11993.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.096867 restraints weight = 9624.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.097575 restraints weight = 8274.264| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.4934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10402 Z= 0.120 Angle : 0.636 8.122 14115 Z= 0.310 Chirality : 0.041 0.182 1609 Planarity : 0.004 0.047 1785 Dihedral : 4.490 55.025 1452 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.10 % Allowed : 0.57 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.24), residues: 1276 helix: 1.58 (0.18), residues: 790 sheet: -0.48 (0.42), residues: 133 loop : -0.88 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 19 TYR 0.019 0.001 TYR B 187 PHE 0.022 0.001 PHE B 163 TRP 0.039 0.002 TRP C 36 HIS 0.003 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (10400) covalent geometry : angle 0.63563 / 0.31 (14111) SS BOND : bond 0.00437 / 0.23 ( 2) SS BOND : angle 1.13349 / 0.60 ( 4) hydrogen bonds : bond 0.03996 / 2.67 ( 634) hydrogen bonds : angle 4.04589 / 2.98 ( 1863) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ASP cc_start: 0.8875 (t0) cc_final: 0.8320 (t70) REVERT: A 205 MET cc_start: 0.8770 (tmm) cc_final: 0.8260 (tmm) REVERT: A 299 TYR cc_start: 0.8918 (m-80) cc_final: 0.8421 (m-80) REVERT: A 444 PHE cc_start: 0.7321 (t80) cc_final: 0.6859 (t80) REVERT: A 540 LEU cc_start: 0.8609 (tp) cc_final: 0.8367 (mt) REVERT: A 544 MET cc_start: 0.7734 (mmm) cc_final: 0.7413 (mmt) REVERT: B 25 LEU cc_start: 0.8680 (tp) cc_final: 0.8353 (tt) REVERT: B 32 LEU cc_start: 0.8247 (mt) cc_final: 0.7660 (mt) REVERT: B 77 TYR cc_start: 0.8667 (t80) cc_final: 0.8367 (t80) REVERT: B 79 MET cc_start: 0.8813 (tmm) cc_final: 0.8449 (tmm) REVERT: B 154 MET cc_start: 0.8648 (ttt) cc_final: 0.8209 (ttt) REVERT: B 199 THR cc_start: 0.8975 (m) cc_final: 0.8639 (m) REVERT: B 203 GLU cc_start: 0.8768 (tt0) cc_final: 0.8465 (tt0) REVERT: B 365 MET cc_start: 0.8169 (tmm) cc_final: 0.7894 (tmm) REVERT: B 436 LEU cc_start: 0.8923 (tp) cc_final: 0.8646 (tp) REVERT: B 559 LEU cc_start: 0.9336 (mt) cc_final: 0.9013 (mt) REVERT: B 569 MET cc_start: 0.6785 (ttm) cc_final: 0.6034 (ttm) REVERT: C 65 LYS cc_start: 0.9042 (ptmt) cc_final: 0.8594 (mttt) REVERT: C 83 MET cc_start: 0.6710 (mmm) cc_final: 0.6109 (mmp) REVERT: C 93 VAL cc_start: 0.8584 (m) cc_final: 0.8145 (p) REVERT: C 94 TYR cc_start: 0.5826 (m-10) cc_final: 0.5462 (m-80) outliers start: 1 outliers final: 0 residues processed: 190 average time/residue: 0.0928 time to fit residues: 25.7252 Evaluate side-chains 143 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 64 optimal weight: 0.6980 chunk 110 optimal weight: 0.5980 chunk 121 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 124 optimal weight: 0.3980 chunk 75 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 120 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 ASN B 431 ASN B 538 HIS C 3 GLN C 80 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.118374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.091194 restraints weight = 26529.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.093708 restraints weight = 16264.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.095423 restraints weight = 11669.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.096439 restraints weight = 9367.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.097319 restraints weight = 8137.442| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.5014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10402 Z= 0.123 Angle : 0.636 8.533 14115 Z= 0.309 Chirality : 0.041 0.175 1609 Planarity : 0.004 0.047 1785 Dihedral : 4.432 53.253 1452 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.10 % Allowed : 0.86 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.24), residues: 1276 helix: 1.59 (0.18), residues: 788 sheet: -0.48 (0.42), residues: 133 loop : -0.88 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 19 TYR 0.018 0.001 TYR B 187 PHE 0.019 0.001 PHE A 478 TRP 0.055 0.002 TRP C 36 HIS 0.003 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (10400) covalent geometry : angle 0.63237 / 0.31 (14111) SS BOND : bond 0.00461 / 0.24 ( 2) SS BOND : angle 4.02492 / 2.17 ( 4) hydrogen bonds : bond 0.03980 / 2.65 ( 634) hydrogen bonds : angle 4.03042 / 2.98 ( 1863) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ASP cc_start: 0.8856 (t0) cc_final: 0.8392 (t70) REVERT: A 205 MET cc_start: 0.8797 (tmm) cc_final: 0.8120 (tmm) REVERT: A 299 TYR cc_start: 0.8915 (m-80) cc_final: 0.8454 (m-80) REVERT: A 444 PHE cc_start: 0.7389 (t80) cc_final: 0.6941 (t80) REVERT: A 540 LEU cc_start: 0.8576 (tp) cc_final: 0.8361 (mt) REVERT: A 544 MET cc_start: 0.7758 (mmm) cc_final: 0.7452 (mmt) REVERT: B 25 LEU cc_start: 0.8633 (tp) cc_final: 0.8331 (tt) REVERT: B 77 TYR cc_start: 0.8623 (t80) cc_final: 0.8365 (t80) REVERT: B 79 MET cc_start: 0.8751 (tmm) cc_final: 0.8433 (tmm) REVERT: B 154 MET cc_start: 0.8454 (ttt) cc_final: 0.8235 (ttp) REVERT: B 199 THR cc_start: 0.8983 (m) cc_final: 0.8634 (m) REVERT: B 347 LYS cc_start: 0.6651 (tptt) cc_final: 0.6162 (tppt) REVERT: B 436 LEU cc_start: 0.8883 (tp) cc_final: 0.8631 (tp) REVERT: B 542 ILE cc_start: 0.9252 (mp) cc_final: 0.9006 (tp) REVERT: B 559 LEU cc_start: 0.9354 (mt) cc_final: 0.9122 (mt) REVERT: B 569 MET cc_start: 0.6640 (ttm) cc_final: 0.5919 (ttm) REVERT: C 65 LYS cc_start: 0.8992 (ptmt) cc_final: 0.8510 (mttt) REVERT: C 83 MET cc_start: 0.6852 (mmm) cc_final: 0.6241 (mmp) REVERT: C 93 VAL cc_start: 0.8498 (m) cc_final: 0.8088 (p) REVERT: C 94 TYR cc_start: 0.5682 (m-10) cc_final: 0.5359 (m-80) outliers start: 1 outliers final: 0 residues processed: 179 average time/residue: 0.0933 time to fit residues: 24.3597 Evaluate side-chains 139 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 116 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 11 optimal weight: 0.4980 chunk 15 optimal weight: 0.6980 chunk 38 optimal weight: 0.4980 chunk 83 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 ASN B 431 ASN C 3 GLN C 80 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.118360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.090779 restraints weight = 27072.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.093304 restraints weight = 16818.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.095047 restraints weight = 12167.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.096087 restraints weight = 9729.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.096991 restraints weight = 8453.744| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.5129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10402 Z= 0.121 Angle : 0.636 8.378 14115 Z= 0.308 Chirality : 0.041 0.177 1609 Planarity : 0.004 0.047 1785 Dihedral : 4.402 52.771 1452 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.10 % Allowed : 0.48 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.24), residues: 1276 helix: 1.64 (0.18), residues: 782 sheet: -0.54 (0.42), residues: 132 loop : -0.77 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 19 TYR 0.018 0.001 TYR B 187 PHE 0.021 0.001 PHE B 163 TRP 0.049 0.002 TRP C 36 HIS 0.003 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (10400) covalent geometry : angle 0.63268 / 0.31 (14111) SS BOND : bond 0.00618 / 0.33 ( 2) SS BOND : angle 3.94305 / 2.13 ( 4) hydrogen bonds : bond 0.03940 / 2.64 ( 634) hydrogen bonds : angle 4.00734 / 2.95 ( 1863) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1716.92 seconds wall clock time: 30 minutes 21.91 seconds (1821.91 seconds total)